Sorry, I lost track of this.
Are you saying that you have some sequences from your input file that are in the Jplace file but not in the sequence_taxa file?
That's weird though I'm may not recall what the intended behavior is.
Is your Jplace the one for the concat marker? Some files are only including results for the house keeping markers (DNGNGWU) that get concatenated into the "concat" marker.
Also your converted jplace will include all the taxa on the tree so the reference sequences wouldn't get reported in the sequence_taxa file. Maybe that's where the differences come from.
So for the 2 forms, are those two headers part of your input file?
they should be of the form <read_name>.<start>.<end>
Start and end being the read coordinates for the match. In the case of the concat marker, it's all the coordinates for the concatenation.
I wasn't able to find K26CO in my references.
I'm not sure I am answering your question correctly... but I hope this helps.